Employing epoxy polymer and pristine and aromatic amine and hydroxyl functionalized SWCNTs in poly(ether ether ketone) (PEEK), novel polymer nanocomposite models were created. Molecular dynamics (MD) simulations were used to explore the interfacial, mechanical, and structural features of single-walled carbon nanotube (SWCNT) reinforced PEEK/epoxy matrix (BM) systems. We used MD simulation techniques to show how covalently functionalizing SWCNTs and blending PEEK with a polymer containing hydroxy‑functional groups can improve the interfacial and mechanical properties of PEEK nanocomposites. This study showed that –CH2C6H4NH2, –CH2C6H4OH group grafted SWCNT improve the interfacial and mechanical properties of PEEK-based nanocomposites due to the formation of hydrogen bonds between the filler materials and the polymer matrix, as well as better filler dispersion into the polymer matrix. The improvement of properties of polymer nanocomposites depends on the extent of the interaction of nanoparticles with the polymer matrix. Aromatic amine and hydroxyl (-CH2C6H4NH2, and -CH2C6H4OH) functionalization of SWCNTs is required for their high-performance engineering applications. Because epoxy polymer has a great ability to form hydrogen bonds with fictionalized SWCNT, adding 10% epoxy polymer to the BM increased the interfacial strength, elastic modulus, and shear modulus of SWCNT composites. This study provides a novel technique to improve the properties of polymer nanocomposites by covalently functionalizing SWCNTs.